NAME¶

pdbfixer - Fix problems in Protein Data Bank files

SYNOPSIS¶

pdbfixer

DESCRIPTION¶

pdbfixer filename [options]

When run with no arguments, it launches the user interface. If any arguments are specified, it runs in command line mode.

OPTIONS¶

-h, --help

show this help message and exit

--pdbid=PDBID

PDB id to retrieve from RCSB [default: None]

--url=URL

URL to retrieve PDB from [default: None]

--output=FILENAME

output pdb file [default: output.pdb]

--add-atoms=ATOMS

which missing atoms to add: all, heavy, hydrogen, or none [default: all]

--keep-heterogens=OPTION

which heterogens to keep: all, water, or none [default: all]

--replace-nonstandard

replace nonstandard residues with standard equivalents

--add-residues

add missing residues

--water-box=X Y Z

add a water box. The value is the box dimensions in nm [example: --water-box=2.5 2.4 3.0]

--ph=PH

the pH to use for adding missing hydrogens [default: 7.0]

--positive-ion=ION

positive ion to include in the water box: Cs+, K+, Li+, Na+, or Rb+ [default: Na+]

--negative-ion=ION

negative ion to include in the water box: Cl-, Br-, F-, or I- [default: Cl-]

--ionic-strength=STRENGTH

molar concentration of ions to add to the water box [default: 0.0]

--verbose

Print verbose output